Since I haven’t seen this mentioned, I just want to say that it is possible to reverse the layering in an autolayout. What you do is that you flip the autolayout frame, then flip the contents. After that you probably want the layer ordered reversed, and there are plugins that can help you with that.
So it is possible but yea, it’s not obvious.
I wasn’t aware of how autolayout children casts shadow. IMHO, children of an autolayout frame shouldn’t cast shadows on it’s siblings. To me it makes sense that all children have the same z-index. Because if the designer is given a tool to control X, but using it actually controls X+Y, then the tool is broken.